OpenSXRaw
Part of the OpenMassSpec stack for mass spectrometry raw-file access.
Rust and Python reader for SCIEX .wiff/.wiff.scan legacy mass
spectrometry data files, with no SCIEX SDK or software dependency.
Covers the TripleTOF and QTRAP instrument families.
Documentation: sigilweaver.app/opensxraw/docs
Known issues and gaps
These apply to opensxraw 0.4.0 and all earlier releases. Figures come from checks run on the public validation corpus (see CORPUS.md).
- m/z values are not reliable on any instrument family. No part of the m/z axis has been validated against a physical reference. Do not use OpenSXRaw m/z values for identification, accurate-mass work, or m/z-based quantification.
- TripleTOF and ZenoTOF m/z values are wrong. The reader applies one
linear
(slope, intercept)calibration per file. In a sample of 48 TOF files, 33 contain negative m/z values (down to about -16) and 8 proteomics runs never exceed m/z 700. In 6 files checked in detail, peaks do not line up with known peptide fragment ions, common background ions, or 1.003 Da isotope spacing; offsets scatter across +-2000 ppm with no cluster. This affects all 170 TripleTOF 5600/5600+/6600 and ZenoTOF 7600.wifffiles in the corpus. The shape of the error is not yet known, so any recalibration you apply must be checked against known ions in your own data. - QTRAP m/z values are raw detector bins, not m/z. They are integers from 0 to about 179,000 and can repeat within a spectrum. This affects all 27 QTRAP 5500/6500+ files in the corpus.
- MS level is wrong on TripleTOF and ZenoTOF. Every scan is labelled
MS2, including MS1 survey scans, so TOF MS2 spectra also have no
precursor m/z and no link to a parent MS1 scan. Treat
ms_levelas unreliable on these files. QTRAP MS levels are correct. - MRM transitions are not reported. QTRAP MRM spectra do not expose their Q1/Q3 transitions, and no SRM chromatograms are produced. Only a TIC chromatogram is available.
.wiff2is not supported. The format is encrypted. The reader currently rejects these files with "Invalid CFB file (wrong magic number)" rather than a message naming.wiff2.- Multi-sample
.wifffiles must be opened withReader::open_sample(Python:opensxraw.open_sample);Reader::openreturns an error. - Not reported or untested: centroid/profile mode (
scan_modeis alwaysNone); negative polarity (handled in code, but no negative-mode file is in the corpus).
What has been checked and holds: the .wiff container and Idx scan
index, retention times (no backwards steps or read failures in a 54-file,
1.16 million-spectrum sample), instrument model, polarity, acquisition
timestamp, and QTRAP MS levels. On QTRAP DDA files, MS2 precursor m/z is
the value the instrument recorded at acquisition (present on 3,084 of
3,087 sampled MS2 scans); it has not been cross-checked against MS1,
because QTRAP MS1 m/z is in raw bins.
Install
Prefer openmassspec-io
with the sciex feature unless you need this parser standalone
(minimal dependencies, or building your own abstraction) - the umbrella
gives you format auto-detection, mzML conversion, and Arrow streaming
across all wired-in vendors for free:
cargo add openmassspec-io --features sciex
pip install openmassspec[sciex]
Standalone:
Rust:
cargo add opensxraw
Python:
pip install opensxraw
Quickstart
Rust:
use opensxraw::reader::Reader;
use openmassspec_core::SpectrumSource;
let mut reader = Reader::open("sample.wiff")?;
for spectrum in reader.iter_spectra() {
let spectrum = spectrum?;
println!("{}: {} peaks", spectrum.native_id, spectrum.mz.len());
}
Python:
import opensxraw
reader = opensxraw.RawReader("sample.wiff")
spectrum = reader.read_spectrum(0)
print(spectrum.ms_level, spectrum.retention_time_sec, len(spectrum.mz))
Reader::open (and RawReader) expects the paired .wiff.scan file to
sit alongside the .wiff file, with .scan appended to the .wiff
filename.
See the docs site for the full guide, format specification, and API reference.
License
Apache-2.0. See LICENSE.
The format specification was developed by binary analysis of public mass-spectrometry datasets (PRIDE accessions). See CORPUS.md and ATTRIBUTION.md.
1 maintainer
Metadata
1 maintainer
Release files for opensxraw 0.4.0
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